Catalyst.jl
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SciML
Chemical reaction network and systems biology interface for scientific machine learning (SciML). High performance, GPU-parallelized, and O(1) solvers in open source software.
Many tests currently assume a certain ordering of species and rates coming from the DSL. We need to update these to use `varmap_to_vars`. This was, for example, causing me issues...
Ideally we would have a way to eliminate algebraic coupling constraints so users could define couplings like ``` sys1.A ~ sys2.B ``` and we can then eliminate one of those...
Quoting from M. Feinberg, Foundations of Chemical Reaction Network Theory, Applied Mathematical Sciences 202, https://doi.org/10.1007/978-3-030-03858-8_7 **Deficiency zero theorem:** > Theorem 7.1.1 (The Deficiency Zero Theorem). Let {S ,C ,R (species,...
ported from my MTK PR I'd like to know the best way to integrate this into the lowering code that exists. Should I add a kwarg in the `convert(
For CME type equations as in https://github.com/SciML/Catalyst.jl/pull/417, it might be worthwhile to look at some of the reachability analysis methods in the literature. One recent example: https://match.pmf.kg.ac.rs/electronic_versions/Match81/n3/match81n3_705-736.pdf
- [x] Eliminate `@reaction_func` and how Hill functions work. (Niklas) - [x] Fix ReactionNetworkImporters. (Sam) - [x] Fix BCR loading and update BCR benchmarks. (Sam) - [x] Work towards previous...
Discourse is suddenly overflowing with mention of packages that could be useful for steady-state / bifurcation analysis. We should look into creating interfaces to use them. [PseudoArcLengthContinuation.jl](https://github.com/rveltz/PseudoArcLengthContinuation.jl) [Bifurcations.jl](https://github.com/tkf/Bifurcations.jl) [HomotopyContinuation.jl](https://github.com/JuliaHomotopyContinuation/HomotopyContinuation.jl) I...
Here is something is on mind for steadystate of `reactionSystem` along with `conservationlaws` ```julia rs::ReactionSystem # some reaction system N = convert(Array{Int},conservationlaws(netstoichmat(rs))) expr₁ = build_function(ratelaw,[species(rs);parameters(rs)]) f₁ = eval(expr₁[2]); out₁ =...
See https://discourse.julialang.org/t/reaction-rate-laws-of-chemical-reaction-networks/56049
As a follow-up to: https://discourse.julialang.org/t/error-when-calculating-rhs-of-reaction-ode-no-method-matching-float64-num/64420 I have a set of 22 aqueous species and 44 reactions I am modelling. The species are transported through a 2D porous medium (by diffusion,...
